Dynamic Flexibility Index Sheds Light on Pin1 Allostery

Abstract

Allostery, which is regulation from distant sites, plays a major role in biology. Pin1 is a modular protein containing a WW domain and a larger peptidyl prolyl isomarase domain (PPIase) that isomerizes phospho-serine/threonine-proline (pS/T-P) motifs, which are critical for signaling within intrinsically disordered loops of cell cycle proteins. Pin1 utilizes allosteric regulations for its function, and binds (pS/T-P) motifs in both domains. The WW domain serves as a docking module, whereas catalysis solely takes place within the PPIase domain. However, enzymatic activity gets enhanced when WW is in the bound form, highlighting PIN1's allosteric regulation. Previous work using NMR and molecular dynamics analysis has shown that binding induced quenching of fast local motions and strengthening of the interaction between two domains, indicated in particular by decrease in flexibility of catalytic loops. Here we present a novel method, the dynamic flexibility index (DFI) analysis, for characterizing the underlying allosteric communications between two domains. DFI measures the resilience of a given position to the perturbations that occur at different parts of the protein, using linear response theory. This index captures multi-dimensional effects when the protein is displaced out of equilibrium. Moreover, we can also identify the allosteric response in dynamic flexibility based on the perturbation response fluctuation profile of the PPIase domain upon WW binding and distinguish the positions that contribute the most. Finally we also explore the mechanistic link between conformational dynamics and co-evolution to identify mutational positions to alter enzymatic function.